Multiple sequence alignment - TraesCS6D01G232600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G232600 chr6D 100.000 5319 0 0 1 5319 326534691 326540009 0.000000e+00 9823.0
1 TraesCS6D01G232600 chr6A 93.345 5364 193 64 63 5319 465226259 465231565 0.000000e+00 7777.0
2 TraesCS6D01G232600 chr6B 93.124 2676 131 28 108 2745 495813994 495811334 0.000000e+00 3873.0
3 TraesCS6D01G232600 chr6B 93.085 2097 59 29 2754 4794 495809776 495807710 0.000000e+00 2990.0
4 TraesCS6D01G232600 chr6B 91.418 536 23 9 4803 5319 495807584 495807053 0.000000e+00 713.0
5 TraesCS6D01G232600 chr1D 89.167 240 16 3 2180 2410 254439691 254439929 1.870000e-74 291.0
6 TraesCS6D01G232600 chr1D 87.805 246 18 4 2180 2413 491423743 491423498 1.460000e-70 278.0
7 TraesCS6D01G232600 chr1D 88.732 71 8 0 2768 2838 379139967 379139897 2.640000e-13 87.9
8 TraesCS6D01G232600 chr5D 88.797 241 17 3 2180 2410 503296555 503296795 2.420000e-73 287.0
9 TraesCS6D01G232600 chr5D 88.017 242 17 4 2180 2410 512413923 512414163 5.250000e-70 276.0
10 TraesCS6D01G232600 chr5D 87.654 243 21 2 2180 2413 6271325 6271083 1.890000e-69 274.0
11 TraesCS6D01G232600 chr5D 92.647 68 5 0 2701 2768 367671685 367671618 1.220000e-16 99.0
12 TraesCS6D01G232600 chr2D 88.750 240 18 2 2180 2410 638429086 638429325 8.720000e-73 285.0
13 TraesCS6D01G232600 chr3D 88.655 238 17 3 2180 2408 235621199 235621435 1.130000e-71 281.0
14 TraesCS6D01G232600 chr3D 93.939 66 4 0 2703 2768 450875180 450875245 3.390000e-17 100.0
15 TraesCS6D01G232600 chr3D 88.889 72 8 0 2768 2839 284818344 284818415 7.340000e-14 89.8
16 TraesCS6D01G232600 chr1A 95.082 61 3 0 2708 2768 352174092 352174152 4.380000e-16 97.1
17 TraesCS6D01G232600 chr1A 89.333 75 7 1 2768 2841 188149064 188148990 5.670000e-15 93.5
18 TraesCS6D01G232600 chr1A 93.333 60 4 0 2709 2768 479830336 479830277 7.340000e-14 89.8
19 TraesCS6D01G232600 chr1A 91.667 60 5 0 2709 2768 188149100 188149041 3.410000e-12 84.2
20 TraesCS6D01G232600 chr1B 90.141 71 7 0 2768 2838 507850430 507850360 5.670000e-15 93.5
21 TraesCS6D01G232600 chr1B 87.500 72 9 0 2768 2839 681775443 681775514 3.410000e-12 84.2
22 TraesCS6D01G232600 chr7A 93.220 59 4 0 2710 2768 692371845 692371787 2.640000e-13 87.9
23 TraesCS6D01G232600 chr7A 93.220 59 4 0 2710 2768 692395691 692395633 2.640000e-13 87.9
24 TraesCS6D01G232600 chr3B 86.667 75 10 0 2765 2839 736142124 736142198 3.410000e-12 84.2
25 TraesCS6D01G232600 chr3A 87.500 72 8 1 2768 2839 372196230 372196300 1.230000e-11 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G232600 chr6D 326534691 326540009 5318 False 9823.000000 9823 100.000000 1 5319 1 chr6D.!!$F1 5318
1 TraesCS6D01G232600 chr6A 465226259 465231565 5306 False 7777.000000 7777 93.345000 63 5319 1 chr6A.!!$F1 5256
2 TraesCS6D01G232600 chr6B 495807053 495813994 6941 True 2525.333333 3873 92.542333 108 5319 3 chr6B.!!$R1 5211

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
283 296 0.107945 AAGATTCGTGCAGGAGGCTC 60.108 55.000 9.34 5.78 45.15 4.70 F
639 655 0.815213 TGGCTGTGCGGATAAGATGC 60.815 55.000 0.00 0.00 0.00 3.91 F
696 712 1.802960 GTATCCTGATGCCTGCGAATG 59.197 52.381 0.00 0.00 0.00 2.67 F
2222 2260 1.431496 CAGCTCGGCCCAAAAATTTG 58.569 50.000 0.00 0.00 37.90 2.32 F
2593 2655 0.884704 TGCGCTCACTTCCCAGTTTC 60.885 55.000 9.73 0.00 0.00 2.78 F
3742 5381 1.005340 GTCGGCAGCTTCTGATCAAG 58.995 55.000 0.00 0.00 32.44 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2230 0.449388 GCCGAGCTGGATTTGAACAG 59.551 55.000 0.00 0.00 42.00 3.16 R
2193 2231 0.960364 GGCCGAGCTGGATTTGAACA 60.960 55.000 0.00 0.00 42.00 3.18 R
2567 2629 2.288666 GGGAAGTGAGCGCATATCAAA 58.711 47.619 11.47 0.00 0.00 2.69 R
3195 4808 0.034186 GTTGGATCATGCCAGGTCCA 60.034 55.000 3.52 3.52 39.52 4.02 R
3960 5599 0.321653 ACAGGCGACCCTTCATGAAC 60.322 55.000 3.38 0.00 40.33 3.18 R
5149 6966 0.828022 ATGGATGGCTTGCATTGGTG 59.172 50.000 1.42 0.00 31.38 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.462280 GCCGACGATCCCGGGTTT 62.462 66.667 22.86 9.73 46.55 3.27
40 41 2.510691 CCGACGATCCCGGGTTTG 60.511 66.667 22.86 19.10 43.05 2.93
41 42 3.192922 CGACGATCCCGGGTTTGC 61.193 66.667 22.86 11.23 40.78 3.68
42 43 3.192922 GACGATCCCGGGTTTGCG 61.193 66.667 22.86 20.88 40.78 4.85
45 46 3.508840 GATCCCGGGTTTGCGCTG 61.509 66.667 22.86 0.00 0.00 5.18
50 51 4.781959 CGGGTTTGCGCTGCCATG 62.782 66.667 9.73 1.02 0.00 3.66
51 52 3.683937 GGGTTTGCGCTGCCATGT 61.684 61.111 9.73 0.00 0.00 3.21
52 53 2.126346 GGTTTGCGCTGCCATGTC 60.126 61.111 9.73 0.00 0.00 3.06
53 54 2.644418 GTTTGCGCTGCCATGTCA 59.356 55.556 9.73 0.00 0.00 3.58
54 55 1.007502 GTTTGCGCTGCCATGTCAA 60.008 52.632 9.73 0.00 0.00 3.18
55 56 1.007502 TTTGCGCTGCCATGTCAAC 60.008 52.632 9.73 0.00 0.00 3.18
56 57 1.732417 TTTGCGCTGCCATGTCAACA 61.732 50.000 9.73 0.00 0.00 3.33
57 58 1.732417 TTGCGCTGCCATGTCAACAA 61.732 50.000 9.73 0.00 0.00 2.83
58 59 1.213537 GCGCTGCCATGTCAACAAT 59.786 52.632 0.00 0.00 0.00 2.71
59 60 0.799534 GCGCTGCCATGTCAACAATC 60.800 55.000 0.00 0.00 0.00 2.67
60 61 0.521867 CGCTGCCATGTCAACAATCG 60.522 55.000 0.00 0.00 0.00 3.34
61 62 0.799534 GCTGCCATGTCAACAATCGC 60.800 55.000 0.00 0.00 0.00 4.58
62 63 0.806868 CTGCCATGTCAACAATCGCT 59.193 50.000 0.00 0.00 0.00 4.93
63 64 0.522626 TGCCATGTCAACAATCGCTG 59.477 50.000 0.00 0.00 0.00 5.18
64 65 0.523072 GCCATGTCAACAATCGCTGT 59.477 50.000 0.00 0.00 41.27 4.40
65 66 1.730121 GCCATGTCAACAATCGCTGTG 60.730 52.381 0.00 0.00 38.67 3.66
66 67 1.609932 CATGTCAACAATCGCTGTGC 58.390 50.000 0.00 0.00 38.67 4.57
67 68 0.523072 ATGTCAACAATCGCTGTGCC 59.477 50.000 0.00 0.00 38.67 5.01
81 82 2.115291 GTGCCGATTTCAGGGGCTC 61.115 63.158 2.72 0.00 46.97 4.70
85 86 1.027357 CCGATTTCAGGGGCTCAATG 58.973 55.000 0.00 0.00 0.00 2.82
98 99 2.359900 GCTCAATGTTCAGGGTTCGAT 58.640 47.619 0.00 0.00 0.00 3.59
100 101 3.181506 GCTCAATGTTCAGGGTTCGATTC 60.182 47.826 0.00 0.00 0.00 2.52
210 219 1.076332 CCTAAACAACCGAAGAGCCG 58.924 55.000 0.00 0.00 0.00 5.52
282 295 0.392193 CAAGATTCGTGCAGGAGGCT 60.392 55.000 9.34 8.07 45.15 4.58
283 296 0.107945 AAGATTCGTGCAGGAGGCTC 60.108 55.000 9.34 5.78 45.15 4.70
302 315 1.137479 TCAGCCGGACCGTATTAAAGG 59.863 52.381 13.94 0.00 0.00 3.11
306 319 1.937899 CCGGACCGTATTAAAGGCAAG 59.062 52.381 13.94 0.00 0.00 4.01
503 519 1.517276 GATCGCGGACGTGTTATCTTG 59.483 52.381 6.13 0.00 41.18 3.02
508 524 3.187700 GCGGACGTGTTATCTTGAAGAT 58.812 45.455 12.86 12.86 38.70 2.40
638 654 0.940126 GTGGCTGTGCGGATAAGATG 59.060 55.000 0.00 0.00 0.00 2.90
639 655 0.815213 TGGCTGTGCGGATAAGATGC 60.815 55.000 0.00 0.00 0.00 3.91
670 686 6.909550 AGTGGTTTAACTTGATTTGCCATA 57.090 33.333 0.00 0.00 0.00 2.74
696 712 1.802960 GTATCCTGATGCCTGCGAATG 59.197 52.381 0.00 0.00 0.00 2.67
702 718 3.687321 ATGCCTGCGAATGCCGTCT 62.687 57.895 0.00 0.00 41.78 4.18
854 870 7.176690 AGGATTGATTGTTTAGTAGTTTGTGGG 59.823 37.037 0.00 0.00 0.00 4.61
973 996 6.349694 GGTTTCTTTTGGCAAAAATGTTGGAA 60.350 34.615 24.15 18.96 34.81 3.53
1273 1296 7.624360 TTGTTGACACTTCTTTGTATCTTGT 57.376 32.000 0.00 0.00 0.00 3.16
1465 1488 2.889852 CGGCTTTGGAGGTAGTAGTTC 58.110 52.381 0.00 0.00 0.00 3.01
1522 1552 3.575965 CTGCTTTGCGGGAGTTAAATT 57.424 42.857 0.00 0.00 0.00 1.82
1530 1560 2.791158 GCGGGAGTTAAATTGTCATGCG 60.791 50.000 0.00 0.00 0.00 4.73
1552 1582 6.746822 TGCGCTCACTTTGTGATAATTAAATG 59.253 34.615 9.73 0.00 41.94 2.32
1840 1870 8.622948 AAGGAAGGAATTCTAACAAAGTGTAG 57.377 34.615 5.23 0.00 0.00 2.74
2005 2037 6.779539 AGAGATCCCATGTTTCAGAAAACTTT 59.220 34.615 0.00 0.00 44.23 2.66
2028 2060 8.746922 TTTGTTTTGCAATATTTCTAGAGCTG 57.253 30.769 0.00 0.00 36.89 4.24
2105 2143 6.247229 TGTAGTTCATGTATTGCCTGGTAT 57.753 37.500 0.00 0.00 0.00 2.73
2107 2145 7.116075 TGTAGTTCATGTATTGCCTGGTATTT 58.884 34.615 0.00 0.00 0.00 1.40
2112 2150 5.421693 TCATGTATTGCCTGGTATTTTTGCT 59.578 36.000 0.00 0.00 0.00 3.91
2116 2154 6.648725 TGTATTGCCTGGTATTTTTGCTTTTC 59.351 34.615 0.00 0.00 0.00 2.29
2163 2201 6.619801 ACCTTGTTCTGTTTATCTTCACAC 57.380 37.500 0.00 0.00 0.00 3.82
2169 2207 7.184106 TGTTCTGTTTATCTTCACACGTTTTC 58.816 34.615 0.00 0.00 0.00 2.29
2192 2230 4.027132 CGTTGTATGTACAATGTCTACGCC 60.027 45.833 14.17 0.00 46.56 5.68
2193 2231 4.994907 TGTATGTACAATGTCTACGCCT 57.005 40.909 0.00 0.00 32.40 5.52
2222 2260 1.431496 CAGCTCGGCCCAAAAATTTG 58.569 50.000 0.00 0.00 37.90 2.32
2379 2425 8.856103 CAAAAGAGTTTTTCTTATTGGAGGGTA 58.144 33.333 0.00 0.00 45.41 3.69
2399 2445 7.466804 AGGGTAGATTGTTGTCCATTTTTAGA 58.533 34.615 0.00 0.00 0.00 2.10
2471 2517 5.964958 AGATGTTAGTTGTTGGATTGTGG 57.035 39.130 0.00 0.00 0.00 4.17
2510 2561 7.391554 TCTTCCACTCAAATCCTCTTATTGTTG 59.608 37.037 0.00 0.00 0.00 3.33
2525 2576 4.836125 ATTGTTGTCAGTGGCTGTTAAG 57.164 40.909 0.00 0.00 32.61 1.85
2526 2577 3.552132 TGTTGTCAGTGGCTGTTAAGA 57.448 42.857 0.00 0.00 32.61 2.10
2527 2578 4.085357 TGTTGTCAGTGGCTGTTAAGAT 57.915 40.909 0.00 0.00 32.61 2.40
2530 2581 3.402110 TGTCAGTGGCTGTTAAGATGTG 58.598 45.455 0.00 0.00 32.61 3.21
2558 2620 4.957684 TGCTCTTAAGGGGTAGCTAATC 57.042 45.455 13.29 0.00 35.95 1.75
2567 2629 2.458620 GGGTAGCTAATCGCCTATCCT 58.541 52.381 0.00 0.00 40.39 3.24
2593 2655 0.884704 TGCGCTCACTTCCCAGTTTC 60.885 55.000 9.73 0.00 0.00 2.78
2618 2680 7.654520 TCTGTTCGCATTAAAAGTAGTTGTAGT 59.345 33.333 0.00 0.00 0.00 2.73
2642 2704 7.671398 AGTGGTGGAAAGAAGAAATGTAATGAT 59.329 33.333 0.00 0.00 0.00 2.45
2739 2801 3.546670 CGTCTGGAATTAGTTGTCGCTAC 59.453 47.826 0.00 0.00 0.00 3.58
2745 2807 4.873827 GGAATTAGTTGTCGCTACAATGGA 59.126 41.667 7.11 0.00 46.84 3.41
2746 2808 5.527582 GGAATTAGTTGTCGCTACAATGGAT 59.472 40.000 7.11 0.00 46.84 3.41
2747 2809 5.991328 ATTAGTTGTCGCTACAATGGATG 57.009 39.130 7.11 0.00 46.84 3.51
2748 2810 3.334583 AGTTGTCGCTACAATGGATGT 57.665 42.857 7.11 0.00 46.84 3.06
2749 2811 4.465632 AGTTGTCGCTACAATGGATGTA 57.534 40.909 7.11 0.00 46.84 2.29
2750 2812 5.023533 AGTTGTCGCTACAATGGATGTAT 57.976 39.130 7.11 0.00 46.84 2.29
2751 2813 5.050490 AGTTGTCGCTACAATGGATGTATC 58.950 41.667 7.11 0.00 46.84 2.24
2752 2814 4.937201 TGTCGCTACAATGGATGTATCT 57.063 40.909 0.00 0.00 43.42 1.98
2799 4411 9.800572 TCTAGATGTATTTCAGTGCTAGATACT 57.199 33.333 0.00 0.00 34.00 2.12
2906 4519 3.659786 TGTAACGACTACTGCTGCATTT 58.340 40.909 1.31 0.00 0.00 2.32
2993 4606 5.765176 TGCTTCTGATTCTGATGTTGTTTG 58.235 37.500 7.83 0.00 0.00 2.93
3042 4655 5.385617 CAAATTGTACTTGTACTGCAGCTC 58.614 41.667 15.27 7.74 0.00 4.09
3082 4695 9.683069 GATTATTTTTCCATGCCTGTATTAGTG 57.317 33.333 0.00 0.00 0.00 2.74
3086 4699 5.702065 TTCCATGCCTGTATTAGTGGTAA 57.298 39.130 0.00 0.00 0.00 2.85
3111 4724 5.452077 GGATCTCACTGTATCCTGTTGTACC 60.452 48.000 1.61 0.00 38.92 3.34
3195 4808 7.718753 GGAATGAGGATGATAACAAGACAGATT 59.281 37.037 0.00 0.00 0.00 2.40
3465 5078 2.027192 TGTATTCCAGGGTGAAGCTGAC 60.027 50.000 0.00 0.00 0.00 3.51
3480 5093 2.430546 CTGACGAAGCTGTGAGTCTT 57.569 50.000 10.88 0.00 34.92 3.01
3512 5125 1.980844 CAAGCGTCAAATGCACACATC 59.019 47.619 0.00 0.00 34.62 3.06
3516 5129 2.095567 GCGTCAAATGCACACATCTCTT 60.096 45.455 0.00 0.00 34.62 2.85
3517 5130 3.485633 CGTCAAATGCACACATCTCTTG 58.514 45.455 0.00 0.00 34.62 3.02
3518 5131 3.240069 GTCAAATGCACACATCTCTTGC 58.760 45.455 0.00 0.00 34.62 4.01
3526 5165 1.538512 ACACATCTCTTGCATGCACAC 59.461 47.619 22.58 0.00 0.00 3.82
3742 5381 1.005340 GTCGGCAGCTTCTGATCAAG 58.995 55.000 0.00 0.00 32.44 3.02
3814 5453 2.316108 TCTGTTTTTCCTTGCCCCTTC 58.684 47.619 0.00 0.00 0.00 3.46
4278 5917 1.666553 TGTTAAGGGCGCACAGTCG 60.667 57.895 14.57 0.00 0.00 4.18
4285 5924 3.181967 GCGCACAGTCGGCAGTAG 61.182 66.667 0.30 0.00 0.00 2.57
4399 6042 6.706270 AGGTTGTTAGCCATAAGTATCATTCG 59.294 38.462 0.00 0.00 0.00 3.34
4523 6167 4.822685 TGCTGGTGCATTTTCCATTATT 57.177 36.364 0.00 0.00 45.31 1.40
4524 6168 4.505808 TGCTGGTGCATTTTCCATTATTG 58.494 39.130 0.00 0.00 45.31 1.90
4623 6290 3.810941 TGACTGGAACGTGTTAATGGAAC 59.189 43.478 0.00 0.00 38.65 3.62
4681 6349 6.147164 CACCAATAGTAAAGCGAAGACTTTGA 59.853 38.462 6.62 0.00 40.08 2.69
4717 6385 2.737376 GACGCACCACCGTTCCTC 60.737 66.667 0.00 0.00 42.24 3.71
4718 6386 3.509137 GACGCACCACCGTTCCTCA 62.509 63.158 0.00 0.00 42.24 3.86
4719 6387 3.041940 CGCACCACCGTTCCTCAC 61.042 66.667 0.00 0.00 0.00 3.51
4933 6726 5.357032 TGCTCTCGATGACATCTACTTAACA 59.643 40.000 13.45 1.07 0.00 2.41
4973 6766 2.389386 CTCGTCTCTGAGGAGGACG 58.611 63.158 4.59 7.76 39.83 4.79
5011 6804 1.495509 CGTGGCCGTGTGTATGTTG 59.504 57.895 0.00 0.00 0.00 3.33
5103 6902 1.272147 ACTGGAGTTCTGAATTGGCCC 60.272 52.381 0.00 0.00 0.00 5.80
5109 6926 2.035626 CTGAATTGGCCCGGTGGT 59.964 61.111 0.00 0.00 0.00 4.16
5140 6957 3.617263 GGTCGCTGTTTGGTTATGTCTAG 59.383 47.826 0.00 0.00 0.00 2.43
5149 6966 7.198390 TGTTTGGTTATGTCTAGTATAGCGTC 58.802 38.462 0.00 0.00 38.99 5.19
5223 7042 2.577911 GCTGCAGAATTTCGCGCC 60.578 61.111 20.43 0.00 0.00 6.53
5269 7088 9.290988 TCCTAACAACAACATCAGCTTTATTTA 57.709 29.630 0.00 0.00 0.00 1.40
5308 7127 4.638421 TGGTGGCGATATCTTTTGTTTAGG 59.362 41.667 0.34 0.00 0.00 2.69
5315 7134 7.979537 GGCGATATCTTTTGTTTAGGGAAAAAT 59.020 33.333 0.34 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.462280 AAACCCGGGATCGTCGGC 62.462 66.667 32.02 0.00 45.60 5.54
23 24 2.510691 CAAACCCGGGATCGTCGG 60.511 66.667 32.02 16.30 46.43 4.79
24 25 3.192922 GCAAACCCGGGATCGTCG 61.193 66.667 32.02 10.13 33.95 5.12
25 26 3.192922 CGCAAACCCGGGATCGTC 61.193 66.667 32.02 10.93 33.95 4.20
28 29 3.508840 CAGCGCAAACCCGGGATC 61.509 66.667 32.02 11.70 0.00 3.36
33 34 4.781959 CATGGCAGCGCAAACCCG 62.782 66.667 11.47 0.00 0.00 5.28
34 35 3.631487 GACATGGCAGCGCAAACCC 62.631 63.158 11.47 4.27 0.00 4.11
35 36 2.126346 GACATGGCAGCGCAAACC 60.126 61.111 11.47 8.48 0.00 3.27
36 37 1.007502 TTGACATGGCAGCGCAAAC 60.008 52.632 11.47 0.00 0.00 2.93
37 38 1.007502 GTTGACATGGCAGCGCAAA 60.008 52.632 11.47 0.00 0.00 3.68
38 39 1.732417 TTGTTGACATGGCAGCGCAA 61.732 50.000 11.47 10.52 0.00 4.85
39 40 1.525718 ATTGTTGACATGGCAGCGCA 61.526 50.000 11.47 4.75 0.00 6.09
40 41 0.799534 GATTGTTGACATGGCAGCGC 60.800 55.000 11.11 0.00 0.00 5.92
41 42 0.521867 CGATTGTTGACATGGCAGCG 60.522 55.000 11.11 3.45 0.00 5.18
42 43 0.799534 GCGATTGTTGACATGGCAGC 60.800 55.000 8.73 8.73 0.00 5.25
43 44 0.806868 AGCGATTGTTGACATGGCAG 59.193 50.000 0.00 0.00 0.00 4.85
44 45 0.522626 CAGCGATTGTTGACATGGCA 59.477 50.000 0.00 0.00 0.00 4.92
45 46 0.523072 ACAGCGATTGTTGACATGGC 59.477 50.000 3.47 0.00 36.31 4.40
46 47 1.730121 GCACAGCGATTGTTGACATGG 60.730 52.381 3.47 0.00 38.16 3.66
47 48 1.609932 GCACAGCGATTGTTGACATG 58.390 50.000 3.47 0.00 38.16 3.21
48 49 0.523072 GGCACAGCGATTGTTGACAT 59.477 50.000 3.47 0.00 38.16 3.06
49 50 1.840630 CGGCACAGCGATTGTTGACA 61.841 55.000 3.47 0.00 38.16 3.58
50 51 1.154413 CGGCACAGCGATTGTTGAC 60.154 57.895 3.47 0.00 38.16 3.18
51 52 0.673333 ATCGGCACAGCGATTGTTGA 60.673 50.000 3.47 0.00 38.16 3.18
52 53 0.168788 AATCGGCACAGCGATTGTTG 59.831 50.000 7.41 0.00 38.16 3.33
53 54 0.881118 AAATCGGCACAGCGATTGTT 59.119 45.000 8.73 0.00 38.16 2.83
54 55 0.447801 GAAATCGGCACAGCGATTGT 59.552 50.000 8.73 1.27 41.94 2.71
55 56 0.447406 TGAAATCGGCACAGCGATTG 59.553 50.000 8.73 0.00 34.28 2.67
56 57 0.729116 CTGAAATCGGCACAGCGATT 59.271 50.000 0.00 0.00 34.98 3.34
57 58 1.091771 CCTGAAATCGGCACAGCGAT 61.092 55.000 0.00 0.00 0.00 4.58
58 59 1.741401 CCTGAAATCGGCACAGCGA 60.741 57.895 0.00 0.00 0.00 4.93
59 60 2.753966 CCCTGAAATCGGCACAGCG 61.754 63.158 0.00 0.00 0.00 5.18
60 61 2.409870 CCCCTGAAATCGGCACAGC 61.410 63.158 0.00 0.00 0.00 4.40
61 62 2.409870 GCCCCTGAAATCGGCACAG 61.410 63.158 0.00 0.00 42.52 3.66
62 63 2.361104 GCCCCTGAAATCGGCACA 60.361 61.111 0.00 0.00 42.52 4.57
63 64 2.044946 AGCCCCTGAAATCGGCAC 60.045 61.111 0.00 0.00 45.56 5.01
64 65 2.135903 TTGAGCCCCTGAAATCGGCA 62.136 55.000 0.00 0.00 45.56 5.69
65 66 0.753111 ATTGAGCCCCTGAAATCGGC 60.753 55.000 0.00 0.00 43.35 5.54
66 67 1.027357 CATTGAGCCCCTGAAATCGG 58.973 55.000 0.00 0.00 0.00 4.18
67 68 1.755179 ACATTGAGCCCCTGAAATCG 58.245 50.000 0.00 0.00 0.00 3.34
79 80 4.002982 TGAATCGAACCCTGAACATTGAG 58.997 43.478 0.00 0.00 0.00 3.02
81 82 3.753272 ACTGAATCGAACCCTGAACATTG 59.247 43.478 0.00 0.00 0.00 2.82
85 86 4.830826 AAAACTGAATCGAACCCTGAAC 57.169 40.909 0.00 0.00 0.00 3.18
98 99 8.726988 CCCTGAATTTATAGACGAAAAACTGAA 58.273 33.333 0.00 0.00 0.00 3.02
100 101 8.040716 ACCCTGAATTTATAGACGAAAAACTG 57.959 34.615 0.00 0.00 0.00 3.16
120 121 4.826556 TGAAAAAGTCCAAACAAACCCTG 58.173 39.130 0.00 0.00 0.00 4.45
210 219 1.743995 CGGAATCGGGTGTGGTTCC 60.744 63.158 0.00 0.00 37.38 3.62
282 295 1.137479 CCTTTAATACGGTCCGGCTGA 59.863 52.381 17.28 0.00 0.00 4.26
283 296 1.578583 CCTTTAATACGGTCCGGCTG 58.421 55.000 17.28 0.00 0.00 4.85
328 341 2.441164 GAGGCGCAGGGAGAGAGA 60.441 66.667 10.83 0.00 0.00 3.10
391 407 2.309504 GCCTAGGGTTTGGAGGGCT 61.310 63.158 11.72 0.00 36.96 5.19
392 408 2.275748 GCCTAGGGTTTGGAGGGC 59.724 66.667 11.72 0.00 0.00 5.19
417 433 0.399949 ATGGCGGATCCTTACCTGGA 60.400 55.000 10.75 0.00 40.82 3.86
426 442 0.819666 GGAGGTTTCATGGCGGATCC 60.820 60.000 0.00 0.00 0.00 3.36
503 519 6.205658 AGCAGGAATCGGCTTATTTTATCTTC 59.794 38.462 0.00 0.00 41.51 2.87
508 524 3.807622 CGAGCAGGAATCGGCTTATTTTA 59.192 43.478 0.00 0.00 44.15 1.52
638 654 7.611213 ATCAAGTTAAACCACTACTACATGC 57.389 36.000 0.00 0.00 0.00 4.06
639 655 9.825972 CAAATCAAGTTAAACCACTACTACATG 57.174 33.333 0.00 0.00 0.00 3.21
973 996 5.880332 TCGCCAAGAGATAAAAGCACTAAAT 59.120 36.000 0.00 0.00 0.00 1.40
1273 1296 4.662468 TGTGCCAATTCTTTAAACTGCA 57.338 36.364 0.00 0.00 0.00 4.41
1522 1552 0.587768 CACAAAGTGAGCGCATGACA 59.412 50.000 11.47 0.76 35.23 3.58
1530 1560 8.638685 ATGCATTTAATTATCACAAAGTGAGC 57.361 30.769 6.01 1.51 46.04 4.26
1552 1582 8.908678 CATAAAATCACATGTAAGTGCATATGC 58.091 33.333 21.09 21.09 39.35 3.14
1588 1618 2.113433 GCGTCCTCTCGAGCTACCA 61.113 63.158 7.81 0.00 0.00 3.25
2005 2037 7.686438 TCAGCTCTAGAAATATTGCAAAACA 57.314 32.000 1.71 0.00 0.00 2.83
2105 2143 5.294060 GGCTGATGAAACAGAAAAGCAAAAA 59.706 36.000 0.00 0.00 39.94 1.94
2107 2145 4.370917 GGCTGATGAAACAGAAAAGCAAA 58.629 39.130 0.00 0.00 39.94 3.68
2112 2150 4.909696 TTTCGGCTGATGAAACAGAAAA 57.090 36.364 0.00 0.00 39.94 2.29
2116 2154 3.904136 ACTTTTCGGCTGATGAAACAG 57.096 42.857 0.00 0.00 40.43 3.16
2192 2230 0.449388 GCCGAGCTGGATTTGAACAG 59.551 55.000 0.00 0.00 42.00 3.16
2193 2231 0.960364 GGCCGAGCTGGATTTGAACA 60.960 55.000 0.00 0.00 42.00 3.18
2222 2260 2.919228 AGTTCATATTCACGAAGCCCC 58.081 47.619 0.00 0.00 0.00 5.80
2338 2380 9.990360 AAAACTCTTTTGTTTGTAAGAAAGGAA 57.010 25.926 0.00 0.00 39.71 3.36
2373 2419 6.590234 AAAAATGGACAACAATCTACCCTC 57.410 37.500 0.00 0.00 0.00 4.30
2410 2456 5.971763 TGGTCAAAAGCATGTTTTACAGTT 58.028 33.333 8.03 0.00 0.00 3.16
2510 2561 3.403038 ACACATCTTAACAGCCACTGAC 58.597 45.455 0.78 0.00 35.18 3.51
2525 2576 5.335976 CCCCTTAAGAGCAAAAGAACACATC 60.336 44.000 3.36 0.00 0.00 3.06
2526 2577 4.524328 CCCCTTAAGAGCAAAAGAACACAT 59.476 41.667 3.36 0.00 0.00 3.21
2527 2578 3.888930 CCCCTTAAGAGCAAAAGAACACA 59.111 43.478 3.36 0.00 0.00 3.72
2530 2581 4.156190 GCTACCCCTTAAGAGCAAAAGAAC 59.844 45.833 3.36 0.00 34.96 3.01
2567 2629 2.288666 GGGAAGTGAGCGCATATCAAA 58.711 47.619 11.47 0.00 0.00 2.69
2593 2655 7.740346 CACTACAACTACTTTTAATGCGAACAG 59.260 37.037 0.00 0.00 0.00 3.16
2618 2680 7.451255 ACATCATTACATTTCTTCTTTCCACCA 59.549 33.333 0.00 0.00 0.00 4.17
2705 2767 7.293073 ACTAATTCCAGACGGAGGTAGTATAA 58.707 38.462 0.00 0.00 44.10 0.98
2799 4411 7.517734 GCGGAATTACTTGTCGCTCAAATATAA 60.518 37.037 0.00 0.00 42.62 0.98
2801 4413 5.277345 GCGGAATTACTTGTCGCTCAAATAT 60.277 40.000 0.00 0.00 42.62 1.28
2803 4415 3.181510 GCGGAATTACTTGTCGCTCAAAT 60.182 43.478 0.00 0.00 42.62 2.32
2906 4519 2.306805 ACCCTCACTCATGCAAAGATGA 59.693 45.455 6.48 0.00 0.00 2.92
2993 4606 8.743099 GCAAGTTACATTGACAAGAGTAAAAAC 58.257 33.333 14.17 7.93 31.55 2.43
3111 4724 3.277715 GCTCTTGGATCCCTTTCTGAAG 58.722 50.000 9.90 4.31 0.00 3.02
3195 4808 0.034186 GTTGGATCATGCCAGGTCCA 60.034 55.000 3.52 3.52 39.52 4.02
3480 5093 4.421033 TTGACGCTTGTGTGTGTAAAAA 57.579 36.364 0.00 0.00 37.00 1.94
3512 5125 4.056740 CCTAGATAGTGTGCATGCAAGAG 58.943 47.826 24.58 10.18 0.00 2.85
3516 5129 3.033909 ACTCCTAGATAGTGTGCATGCA 58.966 45.455 18.46 18.46 0.00 3.96
3517 5130 3.742433 ACTCCTAGATAGTGTGCATGC 57.258 47.619 11.82 11.82 0.00 4.06
3518 5131 5.960113 GGATACTCCTAGATAGTGTGCATG 58.040 45.833 7.70 0.00 32.53 4.06
3814 5453 3.185246 ACTGGAAGGCAGATATCAACG 57.815 47.619 5.32 0.00 39.30 4.10
3960 5599 0.321653 ACAGGCGACCCTTCATGAAC 60.322 55.000 3.38 0.00 40.33 3.18
4256 5895 4.097863 GTGCGCCCTTAACACCGC 62.098 66.667 4.18 0.00 45.99 5.68
4285 5924 4.184629 AGGAACAATAGAATGCAGTCGAC 58.815 43.478 7.70 7.70 0.00 4.20
4399 6042 2.959516 GCAATAGGCCAACAAAAGGAC 58.040 47.619 5.01 0.00 36.11 3.85
4522 6166 8.784994 TGAGCGGTACAAAGATTAAATAAACAA 58.215 29.630 0.00 0.00 0.00 2.83
4523 6167 8.325421 TGAGCGGTACAAAGATTAAATAAACA 57.675 30.769 0.00 0.00 0.00 2.83
4524 6168 7.428472 GCTGAGCGGTACAAAGATTAAATAAAC 59.572 37.037 0.00 0.00 0.00 2.01
4541 6208 1.302033 CCTCAAGTTGCTGAGCGGT 60.302 57.895 0.00 0.00 41.36 5.68
4543 6210 1.303799 ATGCCTCAAGTTGCTGAGCG 61.304 55.000 0.00 0.00 41.36 5.03
4623 6290 5.235186 CCATCGAGCCATTAACAAGAGTAAG 59.765 44.000 0.00 0.00 0.00 2.34
4717 6385 3.121030 CGGAAGCAAGAGCCCGTG 61.121 66.667 0.00 0.00 43.56 4.94
4718 6386 4.394712 CCGGAAGCAAGAGCCCGT 62.395 66.667 0.00 0.00 41.96 5.28
4720 6388 3.978571 GACCCGGAAGCAAGAGCCC 62.979 68.421 0.73 0.00 43.56 5.19
4773 6448 4.777463 AGGATTTCGGGAACAACGATATT 58.223 39.130 0.00 0.00 40.38 1.28
4876 6668 0.962356 CAATCGGGCTGCTTGGTTCT 60.962 55.000 1.94 0.00 0.00 3.01
4933 6726 3.258622 GGACTACACCTCAACAACTAGCT 59.741 47.826 0.00 0.00 0.00 3.32
4973 6766 1.377856 GAGTTTGGAGGAGGCAGCC 60.378 63.158 1.84 1.84 0.00 4.85
5103 6902 1.079875 CGACCGTCCAAATACCACCG 61.080 60.000 0.00 0.00 0.00 4.94
5109 6926 1.801771 CAAACAGCGACCGTCCAAATA 59.198 47.619 0.00 0.00 0.00 1.40
5140 6957 2.286418 GCTTGCATTGGTGACGCTATAC 60.286 50.000 0.00 0.00 0.00 1.47
5149 6966 0.828022 ATGGATGGCTTGCATTGGTG 59.172 50.000 1.42 0.00 31.38 4.17
5223 7042 5.057149 AGGATCTCCGGAATTAACAAATCG 58.943 41.667 5.23 0.00 42.08 3.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.